The Mascot node analyzes the data using the Mascot search engine.

The following table describes the parameters for the Mascot node.

Mascot node parameters

Parameter

Definition

Input Data

 

Protein Database

Specifies the sequence databases to use in the search. The available databases are configured on the Mascot server.

If you use Mascot server 2.3 or later, you can use more than one sequence database for the same search.

Enzyme Name

Specifies the enzyme reagent used for protein digestion.

The following enzymes, set up by the Mascot server, are typical of what might be available:

  • Arg-C
  • Asp-N
  • Asp-N_ambic
  • Chymotrypsin
  • CNBr
  • CNBr+Trypsin
  • Formic_acid
  • Lys-C
  • Lys-C/P
  • LysC+AspN
  • None
  • PepsinA
  • SemiTrypsin
  • TrypChymo
  • (Default) Trypsin
  • Trypsin/P
  • TrypsinMSIPI
  • TrypsinMSIPI/P
  • V8-DE
  • V8-E

Maximum Missed Cleavage Sites

Specifies the maximum number of missed cleavage sites to consider during the digest.

Range: 0 – 9; default: 1

Instrument

Specifies the type of instrument used to acquire the data in the raw data file:

  • ESI-4SECTOR
  • ESI-FTICR
  • ESI-QUAD
  • ESI-QUAD-TOF
  • ESI-TRAP
  • ETD-TRAP
  • FTMS-ECD
  • MALDI Orbitrap
  • MALDI-QIT-TOF
  • MALDI-QUAD-TOF
  • MALDI-TOF-PSD
  • MALDI-TOF-TOF

Note The available instruments might vary on your Mascot server.

Taxonomy

Limits searches to entries from a particular species or group of species. Can speed up a search and ensure that only the match list contains entries from the selected species. Select from the taxonomy database list.

User Email

Specifies the user email address sent to Mascot for a search.

Tolerances

 

Precursor Mass Tolerance

Specifies the mass tolerance used for finding peptide candidates. You can specify the units (Da, mmu, or ppm) for the precursor mass tolerance value.

Range: 0.0001–5.0 Da or 0.04–5000 ppm; default: 10 ppm

Fragment Mass Tolerance

Specifies the mass tolerance used for matching fragment peaks. You can specify the units (Da or mmu) for the fragment mass tolerance value.

Range: 0.0001 Da–2.0 Da; default: 0.8 Da

Use Average Precursor Mass

Determines the type of mass to use for matching the precursor.

  • True: Uses the average precursor mass.
  • (Default) False: Uses the monoisotopic mass.

Modification Groups

 

From Quan Method

Uses the modifications specified within the modification group of the selected quantification method in addition to the specified dynamic and static modifications. You can select these modifications from a dropdown list.

Do not use the modifications that you specify in the modification groups in the selected quantification method as additional dynamic or static modifications. For more information on Mascot quantification methods, see Checking the quantification method.

Dynamic Modifications

 

Show All Modifications

Determines whether to display a short list of the most common modifications or a complete list of all available modifications.

  • True: Displays the short list of the most common modifications.
  • (Default) False: Displays a complete list of all available modifications.

Dynamic Modification

Determines PTMs. The Mascot administrator defines the available modifications.

The application modifies some amino acid residues but not others.

Static Modifications

 

Static Modification

Applies the same specific mass to all occurrences of the named amino acid, as in an exhaustive chemical modification. The Mascot administrator defines the available modifications.

The application applies static modifications universally to every instance on the specified residues or terminus.